NEW YORK (CNN) -- The U.S. government paid more than $1.7 million in defense contracts over the last decade to companies owned by leaders of Warren Jeffs' polygamous sect, with tens of thousands allegedly winding its way back to Jeffs and his church.

The Pentagon had contracts with three companies with ties to Warren Jeffs' polygamous sect.

In fact, some of the deals were made after Jeffs was named to the FBI's "Most-Wanted List" and remained in place while he was on the run.

CNN has learned that between 1998 and 2007, the United States Air Force and Defense Logistics Agency purchased more than $1.7 million worth of airplane parts from three companies owned by members of the Fundamentalist Church of Jesus Christ of Latter-day Saints, which practices polygamy.

Those companies are Utah Tool and Die, Western Precision and NewEra Manufacturing. Today, the companies all operate under the name NewEra Manufacturing, a company based in Las Vegas, Nevada, that says it supplies precision components "for the aerospace, military, medical, recreational and other commercial entities."

"It was my understanding that Western Precision was paying roughly $50,000 a week into the coffers of the church," former sect member Richard Holm said. "It would have been close to $200,000 a month."

Holm said he helped build Western Precision.

A court affidavit signed by a man whose father was the president of Western Precision makes similar allegations.

"During 2003, the amount being sent to the storehouse and the FLDS was around $100,000 per month," John Nielsen said in the October 26, 2005, affidavit. "I have personal knowledge that checks sent to the FLDS Church/Warren Jeffs by [Western Precision] are payable to the FLDS Church and/or Warren Jeffs."

Private investigator Sam Brower, who monitors the sect, said money earned through business dealings with the U.S. government was used to build Jeffs' compounds across the country, including the one recently raided in Eldorado, Texas.

Brower says dozens of companies tied to FLDS are working on contracts with federal or local governments. The Pentagon would confirm only it had contracts with three.

A man who answered the phone at NewEra Manufacturing said it had no comment.

The companies have not been charged with wrongdoing.

Pentagon spokesman Geoff Morrell emphasized that point.

"The Department of Defense awards contracts on the basis of who can most effectively meet our requirements for supplies or services at the most reasonable cost to the taxpayer," he said.

"We do not consider religious affiliation or marital status when selecting vendors, but illegal activity is certainly cause for termination of a contract and perhaps even debarment, which could prevent a contractor from doing business with department ever again."

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He added, "However, DoD is not aware of any criminal allegations against anyone managing the companies in question."

Bob Maginnis, a retired Army lieutenant colonel who now works with a contractor for the Pentagon, said the department does background checks before signing contracts.

"The DoD is obviously abiding by the law, and if we want them to look deeper and discriminate on religious or other activities we need to tell them."

But he added, "If there was a direct line between Jeffs and this company, and his name was associated with a contract, then that should have come to attention of those that were bidding contract."

It's unclear whether Jeffs' name was on any contract, but other senior members of his church were managing the companies.

What might taxpayers think of it all?

"They're just going to shake their head and say here's another example of our tax money going down the drain to support this polygamist in Texas who abuses children and women," Maginnis said. "They'll be appalled and rightly so."

Jeffs is serving time in Utah after his 2007 conviction for being an accomplice to rape, charges related to a marriage he performed in 2001. He also faces trial in Arizona on eight charges of sexual conduct with a minor, incest and conspiracy. See a timeline of Jeffs' life »

The Mormon Church, which gave up plural marriage more than a century ago, has no ties to Jeffs' group.E-mail to a friend